If you have a rental and also improvements, you will need report the basis for the land, the building and the improvements.
Then you need to allocate the selling price to the land, building and improvements.
Yes, the program will compute the depreciation recapture (section 1250) if you have been using the program year after year. If not, you will need to enter that information (basis for depreciation and month/year placed in service)
So in your example, if you made the improvements AFTER starting the rental, the improvements would be a separate asset. If made before, the improvement costs should have been included in the basis of the building.
Yes, the cost basis is always your cost WITHOUT any adjustment for depreciation.
Capital Gains and Section 1250 recapture can be taxed at a different rate.
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